Downloaded from www.microbiologyresearch.org by IP: 54.146.68.70 On: Wed, 05 Apr 2017 04:46:12 Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus Muktak Aklujkar, 1 3 Carla Risso, 2 3 Jessica Smith, 2 Derek Beaulieu, 3 Ryan Dubay, 3 Ludovic Giloteaux, 2 Kristin DiBurro 2 and Dawn Holmes 3 Correspondence Dawn Holmes dholmes@wne.edu Received 11 August 2014 Accepted 25 September 2014 1 Department of Biological Sciences, Towson University, Towson, MD, USA 2 Department of Microbiology, University of Massachusetts, Amherst, MA, USA 3 Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA Ferroglobus placidus was discovered to oxidize completely the aromatic amino acids tyrosine, phenylalanine and tryptophan when Fe(III) oxide was provided as an electron acceptor. This property had not been reported previously for a hyperthermophilic archaeon. It appeared that F. placidus follows a pathway for phenylalanine and tryptophan degradation similar to that of mesophilic nitrate-reducing bacteria, Thauera aromatica and Aromatoleum aromaticum EbN1. Phenylacetate, 4-hydroxyphenylacetate and indole-3-acetate were formed during anaerobic degradation of phenylalanine, tyrosine and tryptophan, respectively. Candidate genes for enzymes involved in the anaerobic oxidation of phenylalanine to phenylacetate (phenylalanine transaminase, phenylpyruvate decarboxylase and phenylacetaldehyde : ferredoxin oxidoreductase) were identified in the F. placidus genome. In addition, transcription of candidate genes for the anaerobic phenylacetate degradation, benzoyl-CoA degradation and glutaryl-CoA degradation pathways was significantly upregulated in microarray and quantitative real-time-PCR studies comparing phenylacetate-grown cells with acetate-grown cells. These results suggested that the general strategies for anaerobic degradation of aromatic amino acids are highly conserved amongst bacteria and archaea living in both mesophilic and hyperthermophilic environments. They also provided insights into the diverse metabolism of Archaeoglobaceae species living in hyperthermophilic environments. INTRODUCTION Proteins account for ~10 % of the biomass of all living organisms (Yokoyama & Matsumura, 2008), and therefore their degradation products play a major role in carbon and nitrogen cycling on the planet. When organisms die, proteins are broken down to their monomers (amino acids) that can serve as carbon, nitrogen, sulfur and energy sources for numerous micro-organisms. Amino acids are also thought to be one of the first biologically relevant molecules ever formed on the planet. It has been proposed that the chemically reducing atmosphere, high temperatures and abundance of precursor gases on the early Earth allowed the formation of certain basic compounds of life, such as amino acids and nucleic acids (Miller, 1953; Parker et al., 2011). Hydrothermal vents are present-day environments that are reminiscent of the conditions that predominated at the onset of life. Therefore, biochemical studies of organisms isolated from hydrothermal vent sediments, such as Ferroglobus placidus and Archaeoglobus fulgidus, can provide consid- erable insight into amino acid metabolism on the early Earth. To date, the majority of studies on amino acid catabolism have focused on the degradation of amino acids in the presence of oxygen, with anaerobic studies being mostly limited to partial oxidation (Baena et al., 1998, 1999; Barker, 1981; Dı ´az et al., 2007; Fonknechten et al., 2010; Russell et al., 2013). However, some anaerobic bacteria that can completely oxidize amino acids to carbon dioxide and respire such inorganic compounds as nitrate, sulfur, sulfate and iron oxides have also been documented (Bak & Widdel, 1986; Ebenau-Jehle et al., 2012; Holmes et al., 3These authors contributed equally to this paper. Abbreviations: qRT, quantitative real-time. A complete record of all oligonucleotide sequences used and raw and statistically treated data files are available in the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/projects/geo/index.cgi), acces- sion number GSE59466. One supplementary figure and 15 supplementary tables are available with the online Supplementary Material. Microbiology (2014), 160, 2694–2709 DOI 10.1099/mic.0.083261-0 2694 083261 Printed in Great Britain